The Delta Smelt (Hypomesus transpacificus) is a small Osmerid native to the San Francisco Bay Delta (Bay-Delta) in California. Delta Smelt population has declined dramatically since the species was declared as endangered in 1993, and now has been listed as critically endangered by the International Union for Conservation of Nature (IUCN). The Bay Delta is a highly modified ecosystem, and the Delta Smelt has been used as an indicator species to assess the overall health of this ecosystem. Recently, a wealth of evidence exists showing that anthropogenic intervention and change in ecosystems leads to alteration in the sensory perception of the environment by aquatic animals compromising survival in highly modified environments. One of the main modalities used by aquatic organisms to assess and survive in the wild is the olfactory system. The olfactory system is involved in pivotal functions such as recognition of predators, kin recognition, mating, foraging and migration. The olfactory system is highly susceptible to contaminants including copper, which is a common contaminant and a well-studied and measurable olfactory toxicant of fish. A link between the olfactory biology and the effects of common contaminants (i.e., copper) found in the Bay Delta on Delta Smelt is lacking. I studied the basic morphological characteristics of the olfactory organ (olfactory rosette) of Delta Smelt using histological, immunohistochemical and ultrastructural techniques; the olfactory mediated behavioral responses to predation related odorants using a behavioral standardized assay and tracking software; and finally, I evaluated morphological changes of the olfactory epithelium and behavioral responses to alarm cues after copper exposures using concentrations of 2, 8 and 32 µg/L and two exposure times (24 and 96 hours). The Delta Smelt can be classified as a macrosmatic fish, based on the morphological features of the olfactory rosette. This fish has multilamellar, paired olfactory rosettes containing a highly specialized olfactory epithelium. The olfactory epithelium was composed by several populations of cells including sensory neurons with distinct morphology and immunocytochemical features. Delta Smelt have a highly sophisticated and sensitive response to predation related odorants. They detect alarm cues in a concentration dependent fashion using olfaction and display specific behaviors (escape responses and freezing) upon detection that all together are considered as olfactory mediated antipredator behaviors. Finally, I demonstrated using histopathological and immunohistochemical techniques that Delta Smelt olfactory epithelium is highly susceptible to copper exposure at concentrations commonly found in the Bay Delta and considered as sublethal. Moreover, there were differential effects on antipredator behaviors after exposure to copper for 24 and 96 hours. Fish exposed to 8 µg/L of copper for 24 hours showed severe damage to the olfactory epithelium and hyperexcitability when presented to alarm cues. At higher concentrations, the epithelium was severely damaged, the antipredator response was absent and there were signs of histological and behavioral toxicity. The results of these experiments demonstrate that Delta Smelt is a highly olfactory species and establishes that copper contamination can impair olfactory responses at environmentally relevant concentrations in this endangered fish.
Profiling multiomic biomarkers in bulk and in situ provides critical information which enables basic research and clinical applications. Unfortunately, most existing profiling methods are limited due to either low multiplexing, sensitivity, costs, or assay complexity. This thesis aims to develop two core technologies that address 1) bulk profiling issues with sensitivity and low throughput as well as 2) in situ profiling issues with low multiplexing capabilities, costs, and limited throughput. To address the first issue, this work introduces a novel liquid biopsy approach that utilizes a platform technology called Integrated Comprehensive Droplet Digital Detection (IC3D). This integrated approach combines microfluidic droplet partitioning technology, fluorescent multiplexed PCR chemistry, and our own unique and rapid particle counting technology to deliver ultrasensitive and ultrafast detection of colorectal cancer-specific genomic biomarkers from minimally processed blood samples. To address the second issue, this work introduces a new spatial multi-omics technology termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA) that integrates a) in situ labeling of molecular markers (e.g. mRNA, proteins) in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, and b) spectra and time-resolved fluorescence imaging and analysis to enable rapid, high-throughput, and cost-effective spatial profiling of multi-omics biomarkers. By utilizing both time and intensity domains for labeling and imaging, this technology seeks to discriminate a vast repertoire of lifetime and spectral components simultaneously within the same pixel or image of a sample to enable highly increased multiplexing capabilities with standard optical systems. Overall, these two technologies represent simple, versatile, and scalable tools which enable more rapid, sensitive, and/or multiplexed protein/transcriptomic analysis.
The majority of vertebrate species diversity are within fish. Marine fish occupy a diverse array of ecological niches including a wide range of salinity tolerance, oxygen tolerance, temperature, depth, desiccation, and light. Fish also have adapted a range of biological traits including varying trophic level, morphology, swimming performance, and reproduction. The microbiome, the total aggregation of microscopic organisms including fungi, bacteria, archaea, and viruses in a specified environment, has largely been studied in mammals, particularly humans from which many associations to disease and health have been demonstrated. Fish microbiome research has largely focused on the gut environment from freshwater captive populations including farmed carp, tilapia, and catfish with marine studies primarily limited to food fish such as salmon. The goal of this dissertation was to develop and apply microbiome tools including sampling methods, DNA extraction, and library preparation (16S and WGSS, whole genome shotgun sequencing) which could be deployed to study a wide range of questions surrounding the parameters which influence the fish mucosal microbiome. With these set of tools, I have asked 1) how do intentional anthropogenic impacts to the water column (organic fertilizer) influence fish gastrointestinal communities, 2) how body sites differ in mucosal communities and changes across environmental gradients, 3) feasibility of developing a model marine fish to use in microbiome experiments to mimic tuna, 4) how the hatchery built environment influences fish mucosal microbiota. My dissertation can be summarized by several key findings. First, the mucosal environments of fish are highly differentiated in that the gill, skin, and digesta communities from the same species of fish are colonized by a large range of phylogenetically diverse microbes. In a freshwater system, organic inputs do influence the fish gut communities but indirectly through nutrient changes. In a wild marine fish, body sites are impacted by different environmental gradients with external body sites like the gill and skin most influenced by temporally variable environmental conditions including sea water temperature. In both freshwater and marine indoor hatchery systems, the built environment plays a critical role in influencing or being influenced by the fish mucosal microbiome.
Parasites and pathogens exert strong selection on their hosts and alter the structure, diversity, and productivity of communities of ecosystems. This paper presents results of a survey of parasite composition and prevalence observed on and within the freshwater hybrids Owens (Siphateles bicolor snyderi) and Lahontan (Siphateles bicolor obesa) Tui Chubs, a native minnow species, in the Eastern Sierra Nevada mountains of California. The Owen and Lahontan Tui Chub is present in many lakes and rivers in Northern California and its parasite community has yet to be characterized. My thesis asks what kinds of parasites are found in the freshwater Tui Chub, which lakes or streams held the highest parasitic loads, and which features of individual fish and the habitat influence parasite density and/or types of parasites. Fish samples were collected in Summer 2019 by PhD student Henry Baker at 10 different sampling sites including freshwater lakes and streams that vary in size, temperature, water chemistry and species present across Owens Valley, California. I dissected 134 individual fish to characterize the ecto- and endo-parasite communities. My results show that two of the locations had significantly higher parasite infection rates than the others, where few macroscopic parasites were observed. These two locations were both geothermal with warmer waters and distinct water chemistry with high salinity and alkalinity. This pattern suggests that some aspects of geothermal habitat favor the parasite life cycle and makes fish in these sites more easily accessible as a host, though the mechanism behind the pattern is unknown. Four main types of visually distinct parasites were found: one adult life-stage tapeworm, one adult life- stage nematode and two metacercaria trematodes, though none were identified taxonomically. The greater parasite infection rates in geothermal habitats may be related to the greater abundance of snails in these sites, which may serve as intermediate hosts to fish parasites. No differences in parasite infection rates or composition were observed between lake and stream habitats. My thesis suggests that the atypical thermal and chemical environment of geothermal springs promotes parasitism in Tui Chub, but that lakes and streams are similar in containing low rates of infection by any parasites among fish.
The natural world is an extraordinary source of diverse organisms and natural product compounds. The use of natural products and their derivatives has been a recurring theme in the discovery and development of new therapeutics. The marine world is vast and contains incredible biological and chemical diversity. Therefore, the oceans have the potential for new discoveries of compounds with medicinal applications. One group of marine organism that has been shown to be a prolific producer of bioactive compounds is the cyanobacteria. This work focuses on the study of new compounds from marine cyanobacteria for their chemical diversity and biological activity. The work in this dissertation focuses on the discovery and characterization of compounds from two different species of cyanobacteria, Leptolyngbya sp. and Moorena producens. These were collected from American Samoa and Puerto Rico, respectively. The characterization of these compounds was achieved through the integration of a variety of techniques including mass spectrometry, advanced NMR technology and genomic information. This analysis led to the characterization of a new ionophore from the Leptolygbya sp. The collection of Moorena producens afforded new analogues of the bioactive compound, curacin A. 2D NMR was an essential aspect in these studies. Therefore, the optimization of different NMR techniques for faster data acquisition was studied in this dissertation for its applications on lower concentrations of natural products. This work highlights the novelty of compounds that can be discovered by the application of the multiple techniques. Additionally, it demonstrates the reduction in time that is possible with new techniques for the experimental acquisition of NMR data. Finally, this dissertation adds to the body of knowledge of the chemistry that originates from the world’s oceans.
Gut microbes provide vital functions for animal hosts. While it is known that host ecology and evolutionary history play a role in shaping gut microbiomes, a majority of studies have focused on mammal hosts. Other vertebrates, including fish, have received little attention. Coral reef fish, in particular, exhibit a wide range of distinct feeding behaviors, evolutionary histories, and geographic distributions that likely correlate with gut microbiome composition and diversity. They also inhabit a fragile ecosystem that is highly sensitive to anthropogenic disturbance—disturbances that are known to impact coral microbiomes but may or may not affect fish gut microbiomes. My thesis leverages a large unprecedented coral reef fish gut microbiome dataset (N=550), where I sampled the gut microbiomes of 20 host species of fish with robust replication spanning three islands across the South Pacific, to better understand how host phylogeny, host diet, and host environment shape vertebrate gut microbiomes. Comparing the gut microbiomes of distantly related hosts can reveal evolutionary and ecological dynamics that govern gut microbiomes across the animal kingdom. Chapter 1 investigates the possible similarities between coral reef fish and mammal gut microbiomes to elucidate any microbial features that may have converged between the two distantly related hosts. Through multivariate and Bayesian analyses, I show that fish and mammal gut microbiomes exhibit striking similarities in composition, particularly within carnivores and herbivores. Specifically, carnivores and herbivore gut microbiomes show more similarities within their diet groups than within their host phylogenies, and share a significant number of ASVs. Herbivore fish and mammal gut microbiomes, in particular, share a significant number of amplicon sequence variants (ASVs) associated with the functional requirements of herbivory, such as Ruminococcus and Treponema. My results indicate that despite 365 million years of evolution and two drastically distinct habitats (terrestrial vs. marine), fish and mammal gut microbiomes have converged on the basis of diet. Expanding on Chapter 1, Chapter 2 moves beyond host phylogeny and diet and aims to isolate and analyze the effects of host habitat on gut microbiome composition and diversity. Previous work on environmental effects acting on animal gut microbiomes largely focused on captive hosts or wild hosts of a single species, potentially ignoring any interactions between host environment and host phylogeny in the wild. Here, I leverage my dataset of coral reef fish gut microbiomes from a diverse range of hosts from three geographically distinct habitats to better understand how host habitat shapes vertebrate gut microbiomes. I find that host habitat significantly shapes fish gut microbiome composition and diversity and these effects are highly dependent on host phylogeny. For example, within the same analyses, a fish such as R. aculeatus, had significantly different gut microbiomes between the three islands, whereas E. merra gut microbiomes were largely unaffected by island location. For the fish gut microbiomes that were significantly impacted by host habitat, many of the associated ASVs were ASVs found in Chapter 1, suggesting that host habitat may also shape gut microbiome function. While comparative approaches on wild hosts are crucial in elucidating generalizable rules that govern animal gut microbiomes, experimental approaches are also imperative to unpack the finer-scale qualities and mechanisms of these rules. Chapter 3 builds on Chapter 2 by leveraging a simulated nutrient enrichment experimental design to further investigate the effects of host environment on gut microbiome composition and diversity. Nutrient enrichment is one of the most threatening consequences of anthropogenic stress on coral reef ecosystems, and the effects of nutrient enrichment on reef fauna gut microbiomes are largely unknown. Here, I artificially enrich the territories (N=40) of a highly abundant, territorial gardening fish, Stegastes nigricans, and use multivariate and differential abundance analyses to elucidate how nutrient enrichment impacts animal gut microbiome composition and diversity. I find that nutrient enrichment effectively “enriches” the gut microbiome, with S. nigricans gut microbiomes in enriched territories exhibiting significantly higher alpha diversities than those in control territories. I also find that these changes are specific to the hindgut and do not occur in the microbiomes of the food source that S. nigricans gardens.
In late 2019, at multiple hatcheries in California’s Central Valley (CCV), offspring of recently spawned fall-run Chinook salmon (Oncorhynchus tshawytscha) exhibited abnormalities in swimming, lethargy, and high early life-stage mortality; the combination of these symptoms is commonly referred to as thiamine deficiency complex (TDC). The cause of thiamine deficiency in Pacific salmonids is hypothesized to be due to a lack of diet heterogeneity and reliance on northern anchovies (Engraulis mordax), containing high levels of thiaminase, a thiamine-cleaving enzyme. Of CCV’s four runs, the endangered Sacramento River winter-run Chinook salmon (WRCS) is perhaps the most vulnerable to thiamine deficiency as any additional stressor will exacerbate current threats to survival. The goal of this study was to evaluate the effect of thiamine supplementation in pre-spawn WRCS females on their offspring egg thiamine concentrations, survival, prevalence of TDC-related symptoms, and physiological performance and behavioral traits. Sixty female WRCS at Livingston Stone National Fish Hatchery were randomly administered either a thiamine injection (n=33; 500 mg/ml thiamine hydrochloride) at a dose of 50 mg/kg body weight or a sham injection (n=27; sterile saline solution) at a volume of 0.127 ml/kg body weight. After spawn, a subset of fertilized eggs from each female were analyzed for thiamine concentration. Eyed embryos were transferred to the University of California, Davis and kept for observations of TDC, survival, and to assess the effects of maternal thiamine treatments on offspring physiology and behavior. Upper thermal tolerance, routine metabolic rate, spontaneous swimming activity, boldness, and anti-predator responses were evaluated in swim-up fry. On average, total egg thiamine concentrations were 5.02 and 34.91 nmol/g for untreated (n=27) and thiamine treated (n=33) females, respectively. Mortality rate of offspring from untreated females averaged 32.97 ± 0.33 %, with rates ranging from 0 to 100%, while offspring from thiamine treated females had a mean mortality rate of less than 1%. Using a binomial logistic regression model, we predicted that a mean total egg thiamine concentration of ~5 nmol/g supports 95% survival within a family (EC95). There were no statistically significant effects of maternal treatment on any of the physiological or behavioral metrics assessed in this study. Overall, we recommend the administration of supplemental thiamine to increase thiamine concentrations past the threshold at which TDC symptoms are commonly observed; however, additional research should be conducted to further examine potential latent effects of thiamine deficiency in Pacific salmonids.
Early American notions of sympathy, largely shaped by Adam Smith’s theory of rational self-interest and fellow feeling, undergird the period’s dominant narrative tropes, socio-political philosophies, and economic ideologies. In this dissertation, I argue that investments in sympathy structure two “domestic” cultural ideals on a watery globe. The first ideal is of a seamlessly productive shipboard society. The second ideal is of an essentially familial national order. To advance these ideals, common sailors, women writers, and political policymakers uphold sympathy as a corrective to sea-based geological or cultural unruliness. In other words, each asserts that domestic stability in a transoceanic system may be gained via a perfection of moral feeling. As I show in two sections, these discrete sentimental narratives on land and at sea confirm antebellum domesticity’s oceanic entanglements. My first section highlights a shipboard domestic ideal that results from oceanic labors that power a U.S.-backed oceanic economy. Specifically, isolated vessels’ socio-material structures direct sailors’ bodies towards affectively cohesive labor. In short, proper feeling at sea is a technical skill as well as a social one. In this system, ideal “sentimental seamen” know exactly how to feel, how to labor, and how to describe those feeling labors. Sailors use novel materialist, labor-based sentimental forms to stake their relative claims to this economic and social ideal. Ultimately, sentimental seamen embody the forms of regulated and monetized feeling that structure age of sail vessels as historical and literary spaces. My second section tracks an antebellum domestic ideal that results from the nation’s reliance on oceanic cultures and economies. Namely, landed writers debate the domestic nation’s place in a “family of nations” via competing definitions of the “villain of all nations.” Within these debates, “pirates of sympathy” are maritime subjects whose incompatibility with state power is due to their supposed incapacity for moral feeling. For some, such figures’ removal protects an ideal national family; for others, the pirate embodies the effects of state violence. As I conclude, this figure’s pervasive literary-historical presence reflects the antebellum era’s shifting and conflicting moral compasses, particularly in relation to maritime slavery and its inheritances. In tracking sentimental seamen and pirates of sympathy, I place two “domestic” ideals on a watery globe. One is a model for ideal domestic laborers at sea. The other is a foil for ideal domestic citizens on land. Both of these figures are defined by their relation to interior, domestic attachments that ripple across and within transoceanic space. In turn, the study of sentimental seamen and pirates of sympathy provide a glimpse of a field I am tentatively calling “terraqueous domestic studies.” Overall, this field treats early American domestic interiority and attachment as fashioned by earth and water together.
Coastal regions lie along a dual ecotone: the boundary of terrestrial and marine ecosystems and at the convergence of fresh and saltwater aquatic ecosystems. These ecotones are biogeochemically active regions that are stimulated by the supply and transport of organic material by way of their aquatic linkages. My dissertation addresses questions of organic matter and nutrient supply, retention, and transformation in the coastal regions of the Santa Barbara Channel with a focus on maintaining sufficiently high nitrogen concentrations to support primary production of kelp forests during low nutrient periods. To examine fluctuations of nitrogen concentrations in nearshore marine waters, and their relationships with physical and biological factors, I conducted intensive sampling for ammonium concentrations during the summer season and found a distinct periodicity in concentrations throughout the full water column in relationship to the tidal cycle. To determine if permeable marine sediment is a source of dissolved inorganic nitrogen to the overlying water column, I conducted a multi-year series of nutrient flux measurements using flow-through sediment bioreactors containing sediment collected near kelp forests and found that they are a source of ammonium and total dissolved nitrogen during the summer season. To investigate organic matter supply to marine sediment, I analyzed coastal sediment samples for evidence of terrestrial organic matter input before, during, and after a period with considerable rainfall that followed a 5 year drought, and I found evidence in both stream and marine sediment of terrestrial organic matter inputs becoming increasingly varied and less degraded over time. Using a Santa Barbara Coastal LTER dataset, I examined carbon and nitrogen in giant kelp tissue to evaluate patterns in nutritional content as they relate to changes in seawater temperature and larger oceanographic indices. I found that the nutritional content of giant kelp tissue collected in the Santa Barbara Channel has declined over the past 17 years, and this decline is correlated with increasing seawater temperatures and fluctuations of the North Pacific Gyre Oscillation index.
Marine aerosols play a large role in the Earth’s climate by cooling via interaction with energy from the sun and altering the chemical and physical properties of clouds. The dissolved organic matter at the ocean surface, where sea spray aerosols and marine gases can be generated, is formed by the microbial loop by circulating nutrients and the ingestion of organisms like phytoplankton or bacteria – with additional inputs from terrestrial sources. The colored fraction of this organic matter, known as marine chromophoric dissolved organic matter, is a subject of considerable interest due to its ability to photosensitize nearby molecules. This indirect photochemical mechanism in the marine environment is not well understood. This dissertation first investigates the composition and properties of this fraction by conducting both simple model experiments in the laboratory and larger experiments such as the use of an indoor ocean-atmosphere facility. The ability to bridge the gap between these two types of study provides this thesis an excellent opportunity to answer various questions regarding the importance of understanding the role of heterogeneous chemistry and photochemistry in our surrounding environment. Lastly, this dissertation applies a similar perspective on photochemistry to explore the multiphase chemistry relevant to indoor environments. Humans spend 20 hours a day on average inside buildings, and while atmospheric pollution has been thoroughly studied, the pollution indoors is widely unknown and unregulated. Inspired by experiments conducted in a real home, various experimental model systems were investigated regarding indoor surfaces. The ultimate goal of the thesis being, to provide insight into the many vital heterogeneous and multiphase processes currently undiscovered in environmental chemistry community.